Lolliplot-class {GenVisR} | R Documentation |
An S4 class for the lolliplot object, under development!!!
Lolliplot(input, transcript = NULL, species = "hsapiens", host = "www.ensembl.org", txdb = NULL, BSgenome = NULL, emphasize = NULL, DomainPalette = NULL, MutationPalette = NULL, labelAA = TRUE, plotALayers = NULL, plotBLayers = NULL, sectionHeights = NULL, verbose = FALSE)
input |
Object of class MutationAnnotationFormat, GMS, VEP, or a data.table with appropriate columns |
transcript |
Character string specifying the ensembl transcript for which to plot, should be a transcript which corresponds to the gene parameter. |
species |
Character string specifying a species when using biomaRt queries |
host |
Character string specifying a host to connect to when using biomaRt queries |
txdb |
A bioconoductor txdb object to annotate amino acid positions, required only if amino acid changes are missing (see details). |
BSgenome |
A bioconductor BSgenome object to annotate amino acid positions, required only if amino acid changes are missing (see details). |
emphasize |
Character vector specifying a list of mutations to emphasize. |
DomainPalette |
Character vector specifying the colors used for encoding protein domains |
MutationPalette |
Character vector specifying the colors used for encoding mutations |
labelAA |
Boolean specifying if labels should be added to emphasized mutations |
plotALayers |
list of ggplot2 layers to be passed to the density plot. |
plotBLayers |
list of ggplot2 layers to be passed to the lolliplot. |
sectionHeights |
Numeric vector specifying relative heights of each plot section, should sum to one. Expects a value for each section. |
verbose |
Boolean specifying if status messages should be reported. |
PlotA
gtable object for the top sub-plot
PlotB
gtable object for the bottom sub-plot
Grob
gtable object storing the arranged plot
primaryData
data.table object storing the primary data
geneData
data.table object storing gene and domain coordinates
# Load a pre-existing data set dataset <- PIK3CA # mode 1, amino acid changes are not present library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(BSgenome.Hsapiens.UCSC.hg38) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene BSgenome <- BSgenome.Hsapiens.UCSC.hg38 keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele", "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification") dataset.mode1 <- dataset[,keep] colnames(dataset.mode1) <- c("chromosome", "start", "stop", "reference", "variant", "sample", "gene", "consequence") # mode 2, amino acid changes are present keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele", "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification", "Transcript_ID", "HGVSp") dataset.mode2 <- dataset[,keep] colnames(dataset.mode2) <- c("chromosome", "start", "stop", "reference", "variant", "sample", "gene", "consequence", "transcript", "proteinCoord") # run Lolliplot object <- Lolliplot(dataset.mode1, transcript="ENST00000263967", species="hsapiens", txdb=txdb, BSgenome=BSgenome) object <- Lolliplot(dataset.mode2, transcript="ENST00000263967", species="hsapiens")